Structure and function of the methanogenic archaeal community in stable cellulose-degrading enrichment cultures at two different temperatures (15 and 30°C)

FEMS Microbiology Ecology

Volumn 30, Issue 4, 1999, Pages 313-326

  Chin, Kuk Jeong ^a   Lukow, Thomas ^a   Stubner, Stephan ^a   Conrad, Ralf ^a  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

Author keywords

CH4 production; Fluorescent in situ hybridization; Phylogenetic tree; Ribosomal RNA; Rice field soil; T RFLP; Temperature optimum

Indexed keywords

DNA;

BACTERIUM; COMMUNITY STRUCTURE; FUNCTIONAL ROLE; METHANOGENESIS; PADDY FIELD; TEMPERATURE EFFECT;

ARTICLE; FLUORESCENCE IN SITU HYBRIDIZATION; METHANOBACTERIUM; METHANOGENESIS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; STRUCTURE ANALYSIS; TEMPERATURE MEASUREMENT;

EID: 0032704282     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(99)00068-9     Document Type: Article

References (33)

1. Großkopf R., Stubner S., Liesack W. Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl. Environ. Microbiol. 64:1998;4983-4989.
2. 2-dependent methanogenesis on washed rice roots. Environ. Microbiol. 1:1999;159-166.
3. Chin K.J., Lukow T., Conrad R. Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil. Appl. Environ. Microbiol. 65:1999;2341-2349.
4. Horz, H.P. (1997) Vergleichende Molekularbiologische Charakterisierung methanogener Populationen an Wurzeln Verschiedener Reisvarietäten. Diploma thesis, University of Marburg, Marburg.
5. Conrad R., Bak F., Seitz H.J., Thebrath B., Mayer H.P., Schütz H. Hydrogen turnover by psychrotrophic homoacetogenic and mesophilic methanogenic bacteria in anoxic paddy soil and lake sediment. FEMS Microbiol. Ecol. 62:1989;285-294.
6. Rajagopal B.S., Belay N., Daniels L. Isolation and characterization of methanogenic bacteria from rice paddies. FEMS Microbiol. Ecol. 53:1988;153-158.
7. Asakawa S., Morii H., Akagawa-Matsushita M., Koga Y., Hayano K. Characterization of Methanobrevibacter arboriphilicus SA isolated from a paddy field soil and DNA-DNA hybridization among M. arboriphilicus strains. Int. J. Syst. Bacteriol. 43:1993;683-686.
8. Asakawa S., Akagawa-Matsushita M., Morii H., Koga Y., Hayano K. Characterization of Methanosarcina mazeii TMA isolated from a paddy field soil. Curr. Microbiol. 31:1995;34-38.
9. Großkopf R., Janssen P.H., Liesack W. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 64:1998;960-969.
10. Frenzel P., Bosse U. Methyl fluoride, an inhibitor of methane oxidation and methane production. FEMS Microbiol. Ecol. 21:1996;25-36.
11. Yao H., Conrad R. Thermodynamics of methane production in different rice paddy soils from China, the Philippines and Italy. Soil Biol. Biochem. 31:1999;463-473.
12. Yao, H., Conrad, R., Wassmann, R. and Neue, H.U. (1999) Effect of soil characteristics on sequential reduction and methane production in sixteen rice paddy soils from China, the Philippines, and Italy. Biogeochemistry (in press).
13. Jetten M.S.M., Stams A.J.M., Zehnder A.J.B. Methanogenesis from acetate - A comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp. FEMS Microbiol. Rev. 88:1992;181-197.
14. Conrad R., Mayer H.P., Wüst M. Temporal change of gas metabolism by hydrogen-syntrophic methanogenic bacterial associations in anoxic paddy soil. FEMS Microbiol. Ecol. 62:1989;265-274.
15. Chin K.J., Conrad R. Intermediary metabolism in methanogenic paddy soil and the influence of temperature. FEMS Microbiol. Ecol. 18:1995;85-102.
16. Holzapfel-Pschorn A., Seiler W. Methane emission during a cultivation period from an Italian rice paddy. J. Geophys. Res. 91:1986;11803-11814.
17. Chin K.J., Rainey F.A., Janssen P.H., Conrad R. Methanogenic degradation of polysaccharides and the characterization of polysaccharolytic clostridia from anoxic rice field soil. Syst. Appl. Microbiol. 21:1998;185-200.
18. Amann R.I., Krumholtz L., Stahl D.A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:1990a;762-770.
19. Amann R., Snaidr J., Wagner M., Ludwig W., Schleifer K.-H. In situ visualization of high genetic diversity in a natural microbial community. J. Bacteriol. 178:1996;3496-3500.
20. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1990b;1919-1925.
21. Raskin L., Stromley J.M., Rittmann B.E., Stahl D.A. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60:1994;1232-1240.
22. Smalla K., Cresswell N., Mendonca-Hagler L.C., Wolters A., van Elsas J.D. Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J. Appl. Bacteriol. 74:1993;78-85.
23. Rotthauwe J.H., Witzel K.P., Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker - molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63:1997;4704-4712.
24. Strunk, O. and Ludwig, W. (1996) ARB: A Software Environment for Sequence Data. http://www.biol.chemie.tu-muenchen.de/pub/ARB/. Technische Universität München, München.
25. Suzuki M.T., Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:1996;625-630.
26. Nübel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R.I., Ludwig W., Backhaus H. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178:1996;5636-5643.
27. Zarda B., Hahn D., Chatzinotas A., Schönhuber W., Neef A., Amann R.I., Zeyer J. Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch. Microbiol. 168:1997;185-192.
28. Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:1995;143-169.
29. Raskin L., Amann R.I., Poulsen L.K., Rittmann B.E., Stahl D.A. Use of ribosomal RNA-based molecular probes for characterization of complex microbial communities in anaerobic biofilms. Water Sci. Tech. 31:1995;261-272.
30. Boone, D.R., Whitman, W.B. and Rouviere, P. (1993) Diversity and taxonomy of methanogens. In: Methanogenesis - Ecology, Physiology, Biochemistry and Genetics (Ferry, J.G., Ed.), pp. 35-80. Chapman and Hall, New York.
31. Westermann P., Ahring B.K., Mah R.A. Temperature compensation in Methanosarcina barkeri by modulation of hydrogen and acetate affinity. Appl. Environ. Microbiol. 55:1989;1262-1266.
32. Isaksen M.F., Joergensen B.B. Adaptation of psychrophilic and psychrotrophic sulfate-reducing bacteria to permanently cold marine environments. Appl. Environ. Microbiol. 62:1996;408-414.
33. Barns S.M., Fundyga R.E., Jeffries M.W., Pace N.R. Remarkable archaeal diversity detected in a Yellowstone national park hot spring environment. Proc. Natl. Acad. Sci. USA. 91:1994;1609-1613.